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TBXT T-box transcription factor T [ Homo sapiens (human) ]

Gene ID: 6862, updated on 5-Mar-2024

Summary

Official Symbol
TBXTprovided by HGNC
Official Full Name
T-box transcription factor Tprovided by HGNC
Primary source
HGNC:HGNC:11515
See related
Ensembl:ENSG00000164458 MIM:601397; AllianceGenome:HGNC:11515
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
T; TFT; SAVA
Summary
The protein encoded by this gene is an embryonic nuclear transcription factor that binds to a specific DNA element, the palindromic T-site. It binds through a region in its N-terminus, called the T-box, and effects transcription of genes required for mesoderm formation and differentiation. The protein is localized to notochord-derived cells. Variation in this gene was associated with susceptibility to neural tube defects and chordoma. A mutation in this gene was found in a family with sacral agenesis with vertebral anomalies. [provided by RefSeq, Sep 2018]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

See TBXT in Genome Data Viewer
Location:
6q27
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (166157656..166168655, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (167527458..167538457, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (166571144..166582143, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901524 Neighboring gene uncharacterized LOC729681 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:166525837-166527036 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:166581481-166582075 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17773 Neighboring gene lncRNA divergent activator of TBXT Neighboring gene NANOG hESC enhancer GRCh37_chr6:166610696-166611243 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:166618881-166620080 Neighboring gene RNA, U6 small nuclear 153, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr6:166637642-166637828 Neighboring gene uncharacterized LOC101929297 Neighboring gene G protein subunit gamma 5 pseudogene 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Neural tube defect
MedGen: C0027794 OMIM: 182940 GeneReviews: Not available
Compare labs
Sacral agenesis-abnormal ossification of the vertebral bodies-persistent notochordal canal syndrome
MedGen: C3810343 OMIM: 615709 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
EBI GWAS Catalog
Genome-wide association identifies the T gene as a novel asthma pharmacogenetic locus.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC104817

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in anterior/posterior axis specification, embryo TAS
Traceable Author Statement
more info
PubMed 
involved_in cardiac muscle cell myoblast differentiation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cell fate specification IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in heart morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in heart morphogenesis IDA
Inferred from Direct Assay
more info
PubMed 
involved_in mesoderm development TAS
Traceable Author Statement
more info
PubMed 
involved_in mesoderm formation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in negative regulation of DNA-binding transcription factor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in primitive streak formation NAS
Non-traceable Author Statement
more info
PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in signal transduction NAS
Non-traceable Author Statement
more info
PubMed 
involved_in somitogenesis IBA
Inferred from Biological aspect of Ancestor
more info
 
Component Evidence Code Pubs
part_of chromatin IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of chromatin IDA
Inferred from Direct Assay
more info
PubMed 
part_of chromatin ISA
Inferred from Sequence Alignment
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
T-box transcription factor T
Names
T brachyury transcription factor
T, brachyury homolog
brachyury protein
protein T

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_012135.1 RefSeqGene

    Range
    5793..15988
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001270484.2NP_001257413.1  T-box transcription factor T isoform 2

    See identical proteins and their annotated locations for NP_001257413.1

    Status: REVIEWED

    Source sequence(s)
    AL627443
    Consensus CDS
    CCDS59045.1
    UniProtKB/Swiss-Prot
    O15178
    Related
    ENSP00000355836.3, ENST00000366871.7
    Conserved Domains (2) summary
    PLN00217
    Location:171279
    PLN00217; predicted protein; Provisional
    pfam00907
    Location:44219
    T-box; T-box
  2. NM_001366285.2NP_001353214.1  T-box transcription factor T isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL627443
    Consensus CDS
    CCDS94030.1
    UniProtKB/TrEMBL
    J3KP65
    Related
    ENSP00000355841.3, ENST00000366876.7
    Conserved Domains (1) summary
    pfam00907
    Location:44219
    T-box; T-box
  3. NM_001366286.2NP_001353215.1  T-box transcription factor T isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL627443
    Consensus CDS
    CCDS94030.1
    UniProtKB/TrEMBL
    J3KP65
    Conserved Domains (1) summary
    pfam00907
    Location:44219
    T-box; T-box
  4. NM_003181.4NP_003172.1  T-box transcription factor T isoform 1

    See identical proteins and their annotated locations for NP_003172.1

    Status: REVIEWED

    Source sequence(s)
    AL627443
    Consensus CDS
    CCDS5290.1
    UniProtKB/Swiss-Prot
    E7ERD6, O15178, Q4KMP4
    Related
    ENSP00000296946.2, ENST00000296946.6
    Conserved Domains (1) summary
    smart00425
    Location:42223
    TBOX; Domain first found in the mice T locus (Brachyury) protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    166157656..166168655 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047419269.1XP_047275225.1  T-box transcription factor T isoform X1

    UniProtKB/Swiss-Prot
    E7ERD6, O15178, Q4KMP4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    167527458..167538457 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054356267.1XP_054212242.1  T-box transcription factor T isoform X1